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Is that happening every time? If so, can you run calibre in debug mode then next time you plan to do it? The logs could give a clue as to what is happening. Also, check the database in case there are any errors when starting.
How long between sending the book and updating the metadata? If you did the update while the send job is running, that might cause problems. You would be fairly unlucky to consistently hit an error, but the two updates could clash. If it looks like that is the problem, I can add a check for running device jobs to prevent the other updates happening at the same time.
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